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9vge

SIRT2 demyristoylation intermediate I structure

Method: X-RAY DIFFRACTION D_max: 66.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vge
deposition_date	2025-06-13
title	SIRT2 demyristoylation intermediate I structure
keywords	Deacylase, Cell Cycle regulation, Metabolic regulation, Hydrolase; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.80 Å
rg_electron	19.66 Å
i0	19771100.00
molecular_weight	33763.0 kDa
excluded_volume	42276 Å³
envelope_volume	48872 Å³
shell_volume	20854 Å³
envelope_diameter	67.3 Å
shell_rg	26.12 Å
envelope_rg	19.98 Å
shape_rg	19.64 Å
total_rg	20.58 Å
total_atoms	2363
n_residues	296
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	66.5 Å
rg_real	20.76 Å
rg_real_error	0.37 Å
i0_real	1.9770e+07
i0_real_error	2.6170e+05
rg_reciprocal	20.76 Å
i0_reciprocal	19770000.0000
total_estimate	0.8919
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.6 Å
skewness	0.337
kurtosis	-0.258
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	3103000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	NAD-dependent protein deacetylase sirtuin-2
formula_weight	34692.0 kDa
ec_number	2.3.1.286,2.3.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2400

SLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Histone H3.1
formula_weight	784.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

APRKQLA

Entity 3 non-polymer

description	NICOTINAMIDE
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	1

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	;[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate ;
formula_weight	755.7 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	25

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6. Citations (1)

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length_a	37.059 Å
length_b	77.646 Å
length_c	55.955 Å
angle_alpha	90.00 °
angle_beta	97.99 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.560 Å
resolution_low	55.474 Å
r_factor	—
r_work	0.2029
r_free	0.2819

fit	/app/data/saxs_computation/vg/9vge/9vge.fit
pddf	/app/data/pr_computation/vg/9vge/9vge.pr.out
profile	/app/data/saxs_computation/vg/9vge/9vge.dat

SIRT2 demyristoylation intermediate I structure

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)